Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study

Battistel, Marcos D.; Pendrill, Robert; Widmalm, Göran; Freedberg, Darón I.

doi:10.1021/jp400402b

Cited by 53 publications

(69 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Therefore at high protein and sugar concentrations, i.e. at gelling conditions, the sugar and protein molecules start competing for hydrogen bonding to residual water; in the case of sucrose, the formation of internal HBs may reduce the strength of the water-sugar network in the protein domain, promoting aggregation [187] and causing the different temperature shifts observed. In short, the sugar-induced changes observed in the early stages of aggregation could originate from modifications of statistical thermodynamics of the systems, more specifically from changes of underlying microscopic structures and dynamics of the whole solvent.…”

Section: Protein Stability and Denaturationmentioning

confidence: 99%

Proteins in Saccharides Matrices and the Trehalose Peculiarity: Biochemical and Biophysical Properties

Cordone¹,

Cupane²,

Emanuele

et al. 2015

COC

View full text Add to dashboard Cite

Immobilization of proteins and other biomolecules in saccharide matrices leads to a series of peculiar properties that are relevant from the point of view of both biochemistry and biophysics, and have important implications on related fields such as food industry, pharmaceutics, and medicine. In the last years, the properties of biomolecules embedded into glassy matrices and/or highly concentrated solutions of saccharides have been thoroughly investigated, at the molecular level, through in vivo, in vitro, and in silico studies. These systems show an outstanding ability to protect biostructures against stress conditions; various mechanisms appear to be at the basis of such bioprotection, that in the case of some sugars (in particular trehalose) is peculiarly effective.Here we review recent results obtained in our and other laboratories on ternary protein-sugar-water systems that have been typically studied in wide ranges of water content and temperature. Data from a large set of complementary experimental techniques provide a consistent description of structural, dynamical and functional properties of these systems, from atomistic to thermodynamic level.In the emerging picture, the stabilizing effect induced on the encapsulated systems might be attributed to a strong biomolecule-matrix coupling, mediated by extended hydrogen-bond networks, whose specific properties are determined by the saccharide composition and structure, and depend on water content.

show abstract

Section: Protein Stability and Denaturationmentioning

confidence: 99%

Proteins in Saccharides Matrices and the Trehalose Peculiarity: Biochemical and Biophysical Properties

Cordone¹,

Cupane²,

Emanuele

et al. 2015

COC

View full text Add to dashboard Cite

show abstract

“…Avoiding buffer anions and removing dissolved CO 2 , both of which catalyze the solvent exchange of hydroxyl protons, are essential. Hydroxyl proton resonances are observable by NMR at lower temperatures and are sharpest below the freezing point of water [16][17][18][19]. This requires the addition of deuteroacetone or another solvent to reduce the freezing point of water, ideally without affecting its solution structure [16].…”

Section: Figmentioning

confidence: 99%

“…This requires the addition of deuteroacetone or another solvent to reduce the freezing point of water, ideally without affecting its solution structure [16]. With sufficient oligosaccharide or salt content, however, solutions could be supercooled without the addition of aprotic solvent providing solution conditions that are more biologically relevant [19].…”

Section: Figmentioning

confidence: 99%

“…Fig. 5 EXSY plots of the α-and β-GlcA hydroxyl protons at mixing times of (a) 6 ms, (b) 12 ms, (c) 18 ms, and (d) 24 ms. As the mixing time increases, the intensity of the exchange cross peaks between the hydroxyl protons and the water resonance increases Battistel et al identified hydroxyl proton hydrogen bonds in aqueous solutions of sucrose, a topic that has been previously debated in the literature [16,27], through direct observation of heteronuclear coupling [19]. A fully aqueous solution containing no organic modifiers was used to measure [ 1 H, 13 C] HSQC-TOCSY cross peaks (Fig.…”

Section: Line Shape Analysis For the Evaluation Of Exchange Rates Andmentioning

confidence: 99%

See 1 more Smart Citation

Methods for Measuring Exchangeable Protons in Glycosaminoglycans

Beecher

Larive

2014

Methods in Molecular Biology

View full text Add to dashboard Cite

Recent NMR studies of the exchangeable protons of GAGs in aqueous solution, including those of the amide, sulfamate, and hydroxyl moieties, have demonstrated potential for the detection of intramolecular hydrogen bonds, providing insights into secondary structure preferences. GAG amide protons are observable by NMR over wide pH and temperature ranges; however, specific solution conditions are required to reduce the exchange rate of the sulfamate and hydroxyl protons and allow their detection by NMR. Building on the vast body of knowledge on detection of hydrogen bonds in peptides and proteins, a variety of methods can be used to identify hydrogen bonds in GAGs including temperature coefficient measurements, evaluation of chemical shift differences between oligo- and monosaccharides, and relative exchange rates measured through line shape analysis and EXSY spectra. Emerging strategies to allow direct detection of hydrogen bonds through heteronuclear couplings offer promise for the future. Molecular dynamic simulations are important in this effort both to predict and confirm hydrogen bond donors and acceptors.

show abstract

“…Using MD simulations, two of these three hydrogen bonds were identified as intramolecular, and one as intermolecular (Figure 8). 26 It is also useful to covalently link two oligosaccharides to increase affinity by trapping transient carbohydratecarbohydrate interactions. NMR analyses of well-designed sugar dimers such as covalently linked Lewis X homodimers and specific ganglioside heterodimers provided atomic-level information of their interaction mechanisms.…”

Section: ç Characterization Of Oligosaccharide Interactionsmentioning

confidence: 99%

New NMR Tools for Characterizing the Dynamic Conformations and Interactions of Oligosaccharides

2013

View full text Add to dashboard Cite

Oligosaccharides play pivotal roles in various molecular recognition events on cell surfaces and in intracellular environments. Although information about the three-dimensional structure of oligosaccharides is crucial for understanding the mechanisms underlying their biological functions and for designing drugs targeting carbohydrate recognition systems, their inherent flexibility hampers detailed conformational analysis. NMR spectroscopy has immense potential for providing atomic details of oligosaccharide structures in solution as well as in complexes with other biomolecules. However, the traditional NMR approach based on local conformational information provided by the nuclear Overhauser effect (NOE) is often precluded by insufficient information about long interatomic distances and hydrogen bonds involving hydroxy groups. To address these issues, new NMR techniques have recently been developed, exploiting the effects of introduced paramagnetic probes and stable isotopes to target oligosaccharides. Lanthanoid tagging and the spin labeling of oligosaccharides induce paramagnetic effects such as pseudocontact shift and paramagnetic relaxation enhancement, offering NOEindependent sources of long-distance information. Deuteriuminduced isotope shifts of neighboring 13 C resonances provide an experimental tool for the identification of hydrogen bonds involving oligosaccharide hydroxy groups. The uniform and position-selective 13 C enrichment of oligosaccharides can be achieved by metabolic labeling using genetically engineered yeast cells. Furthermore, small ganglioside-embedding bicelles have been used for detailed NMR analyses of intermolecular interactions involving glycolipids in membrane environments. These NMR approaches, in conjunction with computational simulation, have opened up new vistas for the analysis of oligosaccharide conformations and interactions at atomic level. Ç IntroductionOligosaccharides, which are formed by the combination of approximately ten types of monosaccharides through various glycosidic linkages, are a major class of essential molecular components in biological systems. By modifying proteins and lipids, oligosaccharides serve as mediators in physiological and pathological molecular recognition events; thus, they are involved in a wide range of cellular processes including proteinfate determination, intercellular communication, and viral infections.1 The detailed characterization of the 3D structures of oligosaccharides in both free and bound states is crucial for understanding their underlying functions and mechanisms and for providing insights into recognition mechanisms that are useful in the design of carbohydrate-based drugs. 2,3Compared to protein structural biology, 3D-structural study of oligosaccharides is still immature, primarily because of high inherent flexibility. The many degrees of freedom in internal motion exhibited by oligosaccharides endow them with conformational adaptability in interacting with various target biomolecules. 2,4 This makes the structural a...

show abstract

Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study

Cited by 53 publications

References 65 publications

Proteins in Saccharides Matrices and the Trehalose Peculiarity: Biochemical and Biophysical Properties

Proteins in Saccharides Matrices and the Trehalose Peculiarity: Biochemical and Biophysical Properties

Methods for Measuring Exchangeable Protons in Glycosaminoglycans

New NMR Tools for Characterizing the Dynamic Conformations and Interactions of Oligosaccharides

Contact Info

Product

Resources

About